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Tuesday, February 28, 2012

Race between phage and bacteria- CRISPR

Let me begin with a note “Survival of the fittest”. There would hardly be anyone who doesn’t know this concept. Bacteria make compounds against fungus and other bacteria’s. Fungus makes compound to suppress the bacteria. Phages attacks the bacteria, bacteria mutate to become resistant to phage. And almost instantaneously the phage also mutates so it can again attack the bacteria. And once again the race begins.

Isn’t that amazing?

For quite some time now, we know of some DNA piece in bacteria that is important in an adaptive immunity to the bacteria. Though there are many cellular immune systems such as Restriction endonucleases, gene repression, DNA modification, receptor modification and the much studied CRISPR system.

CRISPR stands for clustered regularly interspaced short palindromic repeats. This gene represents the struggle for existence between the viruses and the bacteria. The sequence length varies from aprox 20 and 50bp. The system runs along with a team mate called cas (CRISPR associated sequence) and are together called as CRISPR-cas immune system of bacteria. In reality it’s also postulated that this system is an operon regulated feature and hence we can definitely expect a very important role for this. Also CRISPRs have been found to be present in about 40% of all sequenced bacterial genomes, 90% of archaeal genomes. That’s a pretty good number.

So what do we know about the mechanisms of action????

The CRISPR sequence is transcribed into a long RNA which is then cut to make crRNA, (Mature CRISPR RNAs). Each of the individual crRNA has a spacer sequence. While in many bacteria CRISPR spacers contain a large proportion of sequences matching fully or partially genomic sequences of phages. The CRISPR system is divided into 3 stages:

1. Adaptation of the CRISPR via the integration of short sequences of the invaders as spacers
2. Expression of CRISPRs and subsequent processing to small guide RNAs
3. Interference of target DNA by the crRNA guides.

For a detailed discussion on the process, click here. (They have explained it in the best possible way).

I want to summarize so….

The CRISPR sequence contains spacers which are a copy of phage nucleic acid and is inserted into the cell. New phage infections, more spacer registry records are maintained. Each of these new spacer sequences matches some section of the infecting phage genome (called the protospacer). Once a phage enters the cell, if the spacer has the record of infection, immunity is launched by the help of CRSIPR/Cas complex which targets the phage DNA and lyses it. The exact mechanism is not known but appears to be similar to be something like a DNA guided cleavage.

And when the bacteria laugh’s of having acquired resistance, what does the phage do? Yup, he changes his sequence (Mutation) so that the bacterial spacer is no more in agreement. This was shown by experimental data. Some viral genomes can also interfere by integrating right into the CRISPR sequence and thus disrupting their function. So at the angle of fitness cost the bacteria better have a huge record of sequences. To the best of what I know a record of 18 loci, accounting for 1% of the genome is maintained by Methanocaldococcus jannaschii.

Finally, I want to conclude saying that the phylogenetic analysis of sequence in this system can tell us a lot about the history of the bacteria.